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Don't store original VCF header in vcz #367

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Don't store original VCF header in vcz #367

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10 changes: 2 additions & 8 deletions bio2zarr/icf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -891,8 +891,6 @@ def __init__(self, path):
# directory is either a WIP or the wrong format.
with open(self.path / "metadata.json") as f:
self.metadata = IcfMetadata.fromdict(json.load(f))
with open(self.path / "header.txt") as f:
self.vcf_header = f.read()
self.compressor = numcodecs.get_codec(self.metadata.compressor)
self.fields = {}
partition_num_records = [
Expand Down Expand Up @@ -970,9 +968,7 @@ def num_fields(self):

@property
def root_attrs(self):
return {
"vcf_header": self.vcf_header,
}
return {}

def iter_id(self, start, stop):
for value in self.fields["ID"].iter_values(start, stop):
Expand Down Expand Up @@ -1299,10 +1295,8 @@ def init(

self.mkdirs()

# Note: this is needed for the current version of the vcfzarr spec, but it's
# probably going to be dropped.
# Note: the header is no longer stored in vcz, but keep in icf.
# https://github.com/pystatgen/vcf-zarr-spec/issues/15
# May be useful to keep lying around still though?
logger.info("Writing VCF header")
with open(self.path / "header.txt", "w") as f:
f.write(header)
Expand Down
5 changes: 0 additions & 5 deletions tests/test_vcf_examples.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@
import pathlib
import re

import cyvcf2
import numpy as np
import numpy.testing as nt
import pytest
Expand Down Expand Up @@ -53,10 +52,6 @@ def test_filters(self, ds):
],
)

def test_header(self, ds):
vcf = cyvcf2.VCF(self.data_path)
assert ds.attrs["vcf_header"] == vcf.raw_header

def test_source(self, ds):
assert ds.attrs["source"] == f"bio2zarr-{provenance.__version__}"

Expand Down